Error: Synchronization of 'DBMSSQL2.Devqa.sersol.il.pqe\\COREDB3.LibraryDB' and '87P7WK1.Devqa.sersol.il.pqe,1433.LibraryDB' failed: Assembly 'sersolsharedcode,version=1.0.0.0, culture=neutral, publickeytoken=221f68f4f5ae01e4.' was not found in the SQL catalog.

How can I prevent SQL Compare Pro from attempting to synchronize CLR spocs? I can do it interactively but not through the command line.

If I understand correctly, this error is probably happening because the assembly has been excluded. Then you would get this error if an object that depends on that assembly (such as a stored procedure or user-defined function) was being applied to the database without the underlying assembly.